Error about NAs in data

Hi -

I’m fairly new to STAN - apologies if this is a dumb question.
I’m using rstan in R to run some models on a HPC system (because models take many hours to run), but I’m running into a strange error that I can’t seem to figure out:

Error in FUN(X[[i]], …) :
Stan does not support NA (in transectID) in data
failed to preprocess the data; sampling not done

I’ve double-checked the data, and there are no NAs or missing values. When I start running the same model on my laptop, there are no errors and the model seems to runs fine. The only R packages I’m using are plyr and rstan. On my laptop I have R 3.6.1 with rstan version 2.19.2, plyr 1.8.4. On the HPC, it’s running R 3.5.1 with rstan 2.18.1, plyr 1.8.4. Could those differences in the versions of R/rstan be the source of my problem or should I be looking into something else entirely?

Thanks in advance for any advice you might be able to share!

It might be trying to convert a factor called transectID and creating NAs as a result. If so, try doing as.integer(transectID) when you create the list of data to pass to Stan.

Thanks so much for the reply - I really appreciate it. Unfortunately, that didn’t seem to fix the issue and I got the same error. Any other thoughts?

Do you have NA is a level of transectID?

What’s confusing is that transectID is just a vector of integers that index elements in another object. There aren’t any NAs in the transectID vector.

Can you share the data and/or the R code for preparing the data for stan?

Sorry for my delayed response - I’ve been swamped with other projects.

I was able to figure out that the issue isn’t related to the version of R or plyr/rstan being used - I get the same error with newer versions of everything.

Unfortunately I can’t share the data online, but I will try to post a version of the R code I’m using as well as the stan model as soon as I can.

Thanks for your willingness to help me sort out the issue!

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No worries. You can tag me when you post the code.